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Update instructions in README #14

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1566f81
update installation instructions to indicate new RB-jupyter instructions
wrightaprilm Dec 19, 2022
161ca71
Merge branch 'revbayes:master' into master
wrightaprilm Dec 19, 2022
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19 changes: 18 additions & 1 deletion README.md
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Expand Up @@ -9,14 +9,31 @@ python3 -m revbayes_kernel.install
pip3 install metakernel
```

Note that Linux users may have to subsitute
Note that Linux users may have to subsitute

```
python3 -m revbayes_kernel.install install
```

for the middle line.

### RevBayes Compilation

RevBayes [pre-built executables](https://github.com/revbayes/revbayes/releases/tag/v1.2.2-preview1) are designed to work with Jupyter. The `rb` executable must be found using the `which` command or be located using the environment variable, `REVBAYES_JUPYTER_EXECUTABLE`. For instance, you can set the environment variable using

```sh
export REVBAYES_JUPYTER_EXECUTABLE=<revbayes_path>/rb
```

If you are compiling your own copy, RevBayes must be compiled with the `-jupyter` or `-j` flags, like so:

`./build.sh -jupyter true`

This functionality was added to the development branch in commit [15b440a](https://github.com/revbayes/revbayes/commit/15b440a7013e46c08c9472a89fe1e91508c49c3c).


### Deprecated RevBayes Kernel Information

The current version of `revbayes_kernel` calls the RevBayes executable named `rb-jupyter`. Support to compile `rb-jupyter` with the command `./build.sh -jupyter true` was added to the development branch of the main [RevBayes](https://github.com/revbayes/revbayes) repository in commit [6028eb2](https://github.com/revbayes/revbayes/commit/6028eb2925e2910a839e98060768401843a87362). To find `build.sh`, first change your working directory `cd <revbayes_path>/projects/cmake/`.

The `rb-jupyter` binary must be found using the `which` command or be located using the environment variable, `REVBAYES_JUPYTER_EXECUTABLE`. For instance, you can set the environment variable using
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